在细菌基因组中,PSOSP发现了具有独特基因组和宿主特征的普遍SOS独立的prophages
Yali Hao1,2, Mujie Zhang1,2, Xinjuan Lei1,2
1State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China.
iMeta
|October 20, 2025
概括
我们开发了Prophage SOS依赖性预测器 (PSOSP),以将prophages分类为SOS依赖性 (SdPs) 或SOS独立性 (SiPs). PSOSP准确地区分这些类型,揭示了广泛的SiP,在细菌属中具有独特的基因组特征.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 菌体是细菌基因组中集成的病毒DNA,它对宿主生理和生态产生深远的影响.
- 了解菌体诱导机制对于研究菌体与宿主相互作用至关重要.
研究的目的:
- 为了引入Prophage SOS-dependency Predictor (PSOSP),这是一个用于分类prophages的新生物信息学工具.
- 通过分析LexA通过异质学指数 (HI) 结合DNA的诱导模式来预测prophage诱导模式.
主要方法:
- 使用LexA-DNA结合的异质学指数 (HI) 开发PSOSP工具.
- 对PSOSP进行实验验证,以区分SOS-依赖的prophages (SdPs) 和SOS-独立的prophages (SiPs).
- 将PSOSP应用于49333个细菌基因组的大数据集.
主要成果:
- 在区分SdP和SiP方面,PSOSP实现了100%的灵敏度和特异性.
- 在15493个细菌基因组中推断出原诱导模式,确定了11806个SiP.
- 在145个细菌属中发现了SiP,并且与SdP相比显示出不同的基因组特征.
结论:
- PSOSP提供了一个强大的方法来分类prophage诱导模式.
- SiP的流行率和独特特征表明SdP和SiP之间宿主生理学的差异.
- 这项工作提供了对菌体多样性和菌体与宿主相互作用的关键见解.
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